Molecular Structure Analysis Research Articles

Highly carboxylic acid functionalized PIM‐1 by hydrothermal method: Mechanistic study of gas separation properties

AbstractThis paper is dedicated to improve the conversion efficiency of carboxylation for polymers of intrinsic microporous (PIM‐1). According to stable thermal properties of PIM‐1, a hydrothermal method is used for the first time to achieve the carboxylation conversion of PIM‐1 (C‐PIM), achieving a conversion rate of more than 90% at a reaction time of 10 hours, which is nearly five times more efficient than the most efficient conversion process currently available, preserving the film‐forming properties. The completion of the carboxylation conversion is verified using 1H‐NMR and 13C‐NMR, FT‐IR, and organic elemental analysis. It is found that the change in molecular weight affected the film‐forming properties of the membrane material, and the hydrophobicity of the C‐PIM membrane did not decrease compared with C‐PIM membrane reported in previous studies. The effect of C‐PIM on the selectivity of CO2 gas is explained from the microscopic to the macroscopic level by using physical characterization such as molecular structure analysis, XRD, cross‐linkage calculation, pore size and volume distribution, and fractional free volume (FFV) calculation. It verifies that the efficiency of CO2 adsorption and diffusion selectivity for PIM‐1 membranes has been improved by carboxylation, preserving excellent separation, and capture capacity of CO2.

Design and structural characterization of edible double network gels based on wheat bran arabinoxylan and pea protein isolate

Double network (DN) gels based on wheat bran arabinoxylan (WBAX) and pea protein isolate (PPI) were fabricated by a two-step sequential gelation method with laccase catalyzed cross-linking followed by heating. The rheological properties, water holding capacity, microstructure and molecular structure of WBAX/PPI DN gels were investigated. Increasing the concentrations of WBAX and PPI contributed to an enhanced viscoelastic modulus of DN gel, which exhibited an interconnected, bicontinuous and compact structure with smaller pore sizes, as a result of higher cross-linking intensity of WBAX molecules. Low field nuclear magnetic resonance (LF-NMR) results showed that increasing the contents of PPI and WBAX could further restrict the water mobility within DN gel, which was beneficial for enhancing the water holding capacity of gel samples. The molecular structure analysis showed that the crosslinking of WBAX-WBAX, PPI-PPI and WBAX-PPI participated in the formation of WBAX-PPI DN gels.

Split G-Quadruplexes Enhance Nanopore Signals for Simultaneous Identification of Multiple Nucleic Acids.

Assembly of DNA structures based on hybridization like split G-quadruplex (GQ) have great potential for the base-pair specific identification of nucleic acid targets. Herein, we combine multiple split G-quadruplex (GQ) assemblies on designed DNA nanostructures (carrier) with a solid-state nanopore sensing platform. The split GQ probes recognize various nucleic acid sequences in a parallel assay that is based on glass nanopore analysis of molecular structures. Specifically, we split a GQ into two asymmetric parts extended with sequences complementary to the target. The longer G-segment is in solution, and the shorter one is on a DNA carrier. If the target is present, the two separate GQ parts will be brought together to facilitate the split GQ formation and enhance the nanopore signal. We demonstrated detection of multiple target sequences from different viruses with low crosstalk. Given the programmability of this DNA based nanopore sensing platform, it is promising in biosensing.

Experimental and theoretical evaluation of N-pyridoxal-salicylic acid hydrazide derived copper(II) complex with 2-methylimidazole

This article deals with the experimental and theoretical evaluations of N-pyridoxal-salicylic acid hydrazide (H2pd-sah) 1 and its mixed-ligand copper(II) complex with 2-methylimidazole, [Cu(pd-sah)(MeImdH)] 2. The compounds were characterized based on spectral (UV/Vis. IR) methods, powder-XRD, elemental analysis, and molar conductivity measurements. Both compounds' molecular structure and charge analysis were computed through B3LYP with 6-311 G (d, p) and LANL2DZ basic set using the Gaussian 09 W program package. The time-dependent density functional theory (TD-DFT) approach is used in gas-phase electronic transitions of 2 using the LANL2DZ basis set. Also, the computed UV-Vis based upon TD-DFT results and IR spectra were simulated for comparison with the experimental ones. The molecular structure based on theoretical investigation reveals that compound 2 adopts a distorted square planer N2O2 coordination sphere around the Cu(II). The ONO donor atoms of hydrazone moiety and one nitrogen of 2-methylimidazole constitute the N2O2 basal plane. Moreover, the in-vitro antioxidant activity was evaluated by DPPH assay in both compounds. In addition, Molecular docking studies were performed to predict the binding interaction between compound 2 and the Human Serum Albumin HSA (PDB ID: 1H9Z). Communicated by Ramaswamy H. Sarma

Molecular characterization and genetic structure analysis of Coffea arabica and Coffea canephora cultivars from India using SCoT markers

Coffee is the second most traded community after oil and provides a livelihood for more than 125 million people worldwide. It is cultivated in 80 countries spreading over Africa, Asia and Latin America. In recent years, there is an increasing demand for high quality planting material because of the changing dynamics of pests and disease occurrence possibly triggered by climate change. This calls for a better understanding of the existing genetic diversity and its utilization in the breeding program. In this study, we investigated the molecular characterization and genetic structure of twenty coffee cultivars predominantly bred and cultivated in India using Start Codon Targeted (SCoT) molecular markers. Thirty-six SCoT primers amplified 368 bands of which 192 (52.17%) are polymorphic. The mean values of PIC, Resolving power (RP), mean effective multiplex ratio (EMR) and marker index (MI) were 0.27, 16.04, 3.26 and 1.12 respectively indicating the usefulness of these markers for the genetic analysis of coffee cultivars. Four cultivars produced 17 unique bands due to their specific genetic constituents and these bands could be useful for fingerprinting diagnostics. UPGMA clustering based on SCoT markers separated the accessions into two major clusters which accommodated five sub-clusters which are supported by the principal coordinate analysis (PCoA). The STRUCTURE analysis showed K = 5 as the optimum number of groups and completely separated the cultivars mainly according to their development and genetic constitution. Our results represent the first-of-its-kind attempt to shed light on the genetic diversity among coffee cultivars grown in India using the functional marker.

Synthesis, molecular structural, optical, thermal and third harmonic nonlinear optical analysis of Piperazine-1,4-diium bis(2-carboxy-6-nitrobenzoate) tetrahydrate single crystal

Structure and molecular interactions of the title molecular salt (NPP) were established by X-ray diffraction. The elucidated structure model assigns centrosymmetric triclinic arrangement for the molecules. Molecular packing was established through robust O–H⋯O, N–H⋯O and C–H⋯O hydrogen bond network revealing infinite chains, sheets and spiral ladder patterns. The molecular patterns were abridged through C–H … π and π – π linkages expressing several S and R graph set motifs. Single crystals of NPP with defined morphology were grown by the method of slow evaporation from solution from 1: 1 mixed solvent of methanol and water. FT- IR, FT - Raman spectra reinforced the functional groups and with NMR spectra, the protonated-deprotonated nature of the title molecule. UV–visible, Urbach plot, photoluminescence and fluorescence spectral profiles endorsed the electronic transitions and photophysical properties of NPP. Z-scan profile in the closed and open aperture modes was deployed to estimate the magnitude of the third-order nonlinear optical constants. Thermogravimetry coupled with Differential Scanning Calorimetry (DSC) declare the optimal thermal stability of the material till 71.8 °C.

Predicting pesticide dissipation half-life intervals in plants with machine learning models

Pesticide dissipation half-life in plants is an important factor to assessing environmental fate of pesticides and establishing pre-harvest intervals critical to good agriculture practices. However, empirically measured pesticide dissipation half-lives are highly variable and the accurate prediction with models is challenging. This study utilized a dataset of pesticide dissipation half-lives containing 1363 datapoints, 311 pesticides, 10 plant types, and 4 plant component classes. Novel dissipation half-life intervals were proposed and predicted to account for high variations in empirical data. Four machine learning models (i.e., gradient boosting regression tree [GBRT], random forest [RF], supporting vector classifier [SVC], and logistic regression [LR]) were developed to predict dissipation half-life intervals using extended connectivity fingerprints (ECFP), temperature, plant type, and plant component class as model inputs. GBRT-ECFP had the best model performance with F1-microbinary score of 0.698 ± 0.010 for the binary classification compared with other machine learning models (e.g., LR-ECFP, F1-microbinary= 0.662 ± 0.009). Feature importance analysis of molecular structures in the binary classification identified aromatic rings, carbonyl group, organophosphate, =C-H, and N-containing heterocyclic groups as important substructures related to pesticide dissipation half-lives. This study suggests the utility of machine learning models in assessing the environmental fate of pesticides in agricultural crops.

Co-gasification of refuse-derived fuels and bituminous coal with oxygen/steam blend to hydrogen rich gas

The gasification technology of refuse-derived fuels (RDF) can represent a future alternative to the global hydrogen production and a pathway for the development of the circular economy. The paper presents an innovative way of utilizing RDF through their oxygen/steam co-gasification with bituminous coal to hydrogen rich gas. Five different RDF samples (RDF1÷RDF5) were investigated. The in-depth analyses of the co-gasification of bituminous coal blends with different amounts of RDF (10, 15 and 20%w/w) under various temperature conditions were conducted with the application of Hierarchical Clustering Analysis (HCA). The results of the research study revealed a decrease in the total gas yield as well as in the hydrogen yield observed with the increase in the RDF fraction in the fuel blend. The lowest hydrogen yield and the highest carbon conversion were noted for the co-gasification tests of coal blends with 20%w/w for all the studied RDFs. The SEM-EDS (Scanning Electron Microscopy with Energy Dispersive Spectroscopy) and WDXRF (Wavelength Dispersive X-ray Fluorescence) results showed a significantly higher H2 yield in RDF2 co-gasification with coal in comparison with all the remaining RDFs, due to the higher concentration of calcium in the sample. The molecular structure analysis of polymers using Fourier transform infrared spectroscopy (FTIR) demonstrated that the most prevalent synthetic polymers in RDF2 are polyethylene terephthalate and polyvinyl chloride characterized by the lowest thermal stability compared to polyethylene and polypropylene.

Clinical and genetic features of Charcot-Marie-Tooth disease patients with IGHMBP2 mutations

Autosomal recessive Charcot-Marie-Tooth disease Type 2S (AR-CMT2S) caused by IGHMBP2 mutation was first reported in 2014, and an increasing number of cases have been reported in the past eight years. We detected 15 distinct IGHMBP2 mutations among 8 typical AR-CMT2S families in our cohort of 178 Chinese CMT2 families using Sanger sequencing and next-generation sequencing (NGS), making IGHMBP2 mutations the most frequent cause of AR-CMT2 in our cohort. From 2014 to 2022, 34 AR-CMT2S families, including 45 patients and 47 different mutations, were reported. One third of identified mutations represented presumed loss-of-function variants (nonsense, frameshift and splicing), while two-thirds were missense changes which clustered in the helicase and ATPase domains. The age at onset ranged from 0.11 years to 20 years (mean±SD: 3.76±3.93 years) and the infantile (0–2 years) onset group accounted for the most patients (51.1%). The initial symptoms included muscle weakness (15, 33.3%), delayed milestones (9, 20%), feet deformity (8, 17.8%), gait disturbance (8, 17.8%), feet drop (7, 15.6%), frequent falls (3, 6.7%), hypotonia (2, 4.4%) and thenar atrophy (1, 2.2%). Molecular structural model analysis of 26 missense IGHMBP2 mutations using PyMOL software revealed that six mutations were close to the RNA-binding channel, eight mutations were in or close to the nucleotide-binding pocket. Based on available limited clinical information, it seems possible that missense changes located in or close to these motifs might be linked to a more severe clinical outcome. In conclusion, IGHMBP2 mutation screening should recommended for early-onset, moderately or severely affected, and sporadic or AR-CMT2 patients. A tiny minority of patients were relatively late onset and mild affected, which should be given more attention in genetic diagnosis and treatment. While our preliminary analysis suggests a potential link between the localization of missense mutations and clinical presentation, definition of genotype-phenotype relationships will require harmonized clinical information from a larger series of patients.

Molecular evolution and structural analyses of the spike glycoprotein from Brazilian SARS-CoV-2 genomes: the impact of selected mutations

The COVID-19 pandemic caused by SARS-CoV-2 has reached by February 2022 more than 380 million cases and 5.5 million deaths worldwide since its beginning in late 2019, leading to enhanced concern in the scientific community and the general population. One of the most important pieces of this host-pathogen interaction is the spike protein, which binds to the hACE2 cell receptor, mediates the membrane fusion and is the major target of neutralizing antibodies against SARS-CoV-2. The multiple amino acid substitutions observed in this region, specially in RBD have enhanced the hACE2 binding affinity and led to several modifications in the mechanisms of SARS-CoV-2 pathogenesis, improving the viral fitness and/or promoting immune evasion, with potential impact in the vaccine development. In this work, we identified 48 sites under selective pressures, 17 of them with the strongest evidence by the HyPhy tests, including VOC related mutation sites 138, 142, 222, 262, 484, 681, and 845, among others. The coevolutionary analysis identified 28 sites found not to be conditionally independent, such as E484K-N501Y. The molecular dynamics and free energy estimates showed the structural stabilizing effect and the higher impact of E484K for enhanced binding affinity between the spike RBD and hACE2 in P.1 and P.2 lineages (specially with L452V). Structural changes were also identified in the hACE molecule when interacting with B.1.1.7 RDB. Despite some destabilizing substitutions, a stabilizing effect was identified for the majority of the positively selected mutations. Communicated by Ramaswamy H. Sarma

Synthesis, Molecular Structure, Thermal and Spectroscopic Analysis of a Novel Bromochalcone Derivative with Larvicidal Activity

Chalcones belong to the flavonoids family and are natural compounds which show promising larvicidal property against Aedes aegypti larvae. Aiming to obtain a synthetic chalcone derivative with high larvicidal activity, herein, a bromochalcone derivative, namely (E)-3-(4-butylphenyl)-1-(4-bromophenyl)-prop-2-en-1-one (BBP), was designed, synthesized and extensively characterized by 1H- and 13C- nuclear magnetic resonance (NMR), infrared (IR), Raman spectroscopy, mass spectrometry (MS), ultraviolet–visible spectroscopy (UV-Vis), thermogravimetric analysis (TGA), differential scanning calorimetry (DSC), and X-ray diffraction. Further, the quantum mechanics calculations implemented at the B3LYP/6–311+G(d)* level of the theory indicate that the supramolecular arrangement was stabilized by C–H⋯O and edge-to-face C–H⋯π interactions. The EGAP calculated (3.97 eV) indicates a good reactivity value compared with other similar chalcone derivatives. Furthermore, the synthesized bromochalcone derivative shows promising larvicidal activity (mortality up to 80% at 57.6 mg·L−1) against Ae. aegypti larvae.

Molecular Structure Analysis and Mercury Adsorption Mechanism of Iron-Based Modified Biochar

The elemental composition, molecular skeleton vibration mode, and carbon-chain structure of iron-based modified biochar demercuration materials were studied on a microscopic scale using a variety of characterization methods. A three-dimensional molecular structure monomer model of iron-based modified biochar with defective carbon rings doped with high-valence metals was constructed. The reaction path of Hg0 adsorption on the surface of iron-based modified biochar was studied. The activation energy barrier and the rate-determining step of Hg0 adsorption on the surface of iron-based modified biochar were determined. Then, two reaction mechanisms and the corresponding bonding mechanism of Hg0 adsorption on modified biochar were proposed. In addition, the feasibility of regenerating biochar with different load ratios was verified and the regeneration reaction mechanism of inactivated biochar at different adsorption sites was revealed. The results show that the molecular structure of iron-based modified biochar is dominated by polycyclic aromatic carbon, and its molecular formula is C45H24O12NFe. Adsorption sites on iron-based modified biochar surface are not unique. A heterogeneous oxidation reaction occurs between Hg0, a Lewis base, and modified biochar, a Lewis acid. Hg-O-Fe-Ox–1 and the complex Hg-OM are the main products of Hg0 oxidation. Oxygen vacancies with electrons are the chemical adsorption sites, and Fe3+, lattice oxygen, and chemisorbed oxygen are the main oxidation sites on the modified biochar. The coupling of these four constituents enables the adsorption and oxidation of Hg0. Inactivated biochar can be regenerated by supplementing the lost lattice oxygen or chemisorbed oxygen with more oxygen. The maximum mercury adsorption efficiency decreased to 90% of the primary mercury adsorption efficiency. This study quantitatively revealed the mercury adsorption mechanism of iron-based modified biochar and the regeneration mechanism of inactivated biochar, laying a foundation for further improvements in the mercury adsorption efficiency of metal-modified biochar.

Molecular phylogenetic and morphometric analysis of population structure and demography of endangered threadfin fish Eleutheronema from Indo-Pacific waters

The threadfin Eleutheronema are the important fishery resources in Indo-Pacific regions and classified as the endangered species with considerable conservation values. Their genetic diversity and population structure remain essentially unknown but are critical for the proper management and sustainable harvests of such important fisheries. Here, the mitochondrial DNA sequences of CO1 and 16s rRNA were determined from 75 individuals of Eleutheronema tetradactylum and 89 individuals of Eleutheronema rhadinum collected from different locations of South China Sea and Thailand coastal waters. Genetic diversity analysis revealed that both E. tetradactylum (Haplotype diversity, H = 0.105–0.211; Nucleotide diversity, π = 0.00017–0.00043) and E. rhadinum (H = 0.074–0.663, π = 0.00013–0.01088) had low diversity. Population structure analysis demonstrated the shallow genetic differentiation among the South China Sea populations. The limited communication between China and Thailand populations caused the high genetic differentiation in all groups due to the low dispersal ability. Reconstruction of CO1 phylogenetic relationships and demographic studies across Indo-West-Pacific regions provided strong evidence for a shared common origin or ancestor of E. tetradactylum and E. rhadinum. Eleutheronema rhadinum were further subdivided into two distinct genetic lineages, with Clade A dominantly distributing in Thailand and Malaysia and Clade B distributing in China coastal waters. Phenotypic divergence, characterized mainly by the depth of caudal peduncle and length of caudal peduncle, was also observed for all populations, which was possibly associated with specific local adaptations to environmental changes. Our study suggested a strong need for the development of proper fishery management strategies and conservation actions for the imperiled Eleutheronema species.

Analysis of Pyrolysis Performance and Molecular Structure of Five Kinds of Low-Rank Coals in Xinjiang Based on the TG-DTG Method.

Taking five coal samples (FCSs) in Xinjiang as the research object, characterizations such as proximate analysis, ultimate analysis, Fourier transform infrared (FTIR), and thermogravimetry-differential thermal analysis (TG-DTG) were carried out. The Coats–Redfern model was used to simulate pyrolysis kinetics of FCSs under different reaction orders (ROs). The results showed that except for HSBC, the R2 of the other four coal samples are all higher than 0.9, which showed a good correlation effect. FCSs present similar reaction activation energy in the same RO and temperature range. Results of FTIR showed that the hydroxyl groups of FCSs, in the range of 3100–3600 cm–1, were mainly self-associated hydroxyl hydrogen bonds and hydroxyl π bonds, and they occupied over 63%. Among them, the pyrolysis characteristic index (D) of XBC was 4.139 × 10–6, higher than those of other samples, and it showed good pyrolysis performance. Moreover, by reducing the temperature range appropriately, the fitting results showed a better correlation effect.

2-Aminopyridine Cadmium (II) meso-chlorophenylporphyrin coordination compound. Photophysical properties, X-ray molecular structure, antimicrobial activity, and molecular docking analysis

2-Aminopyridine Cadmium (II) meso-chlorophenylporphyrin coordination compound. Photophysical properties, X-ray molecular structure, antimicrobial activity, and molecular docking analysis

Molecular modeling and structural analysis of some tetrahydroindazole and cyclopentanepyrazole derivatives as COX-2 inhibitors

In an attempt to rationalize the search for new potential anti-inflammatory compounds on the COX-2 enzyme, we carried out an in silico protocol that successfully combines the prediction of physicochemical and pharmacokinetic properties, molecular docking, molecular dynamic simulation, and free energy calculation. Starting from a small library of compounds synthesized previously, it was found that 70% of the compounds analyzed satisfy with the associated values to physicochemical principles as key evaluation parameters for the drug-likeness; all the compounds presented good gastrointestinal absorption and cerebral permeability and they showed an interaction with the Arg 106 residue of the COX-2 isoenzyme. Finally, it was obtained that compound 3ab has a binding mode, binding energy, and stability in the active site of COX-2 like the reference drug celecoxib, suggesting that this compound could become a powerful candidate in the inhibition of the COX-2 enzyme. In addition, we realized the crystallographic analysis of compounds 3j, 3r, and 3t defining the crystal parameters and the Packing interactions.

Hirshfeld surface analysis and quantum chemical study of molecular structure of phosphate

ABSTRACT. In this present study, Density fuctional theoretical computations are performed at (B3LYP, PBEPBE), HF and MP2 level with 3-21G basis sets to derive optimized geometry and bonding features. The calculated geometrical parameters have been compared with experimental data. The intermolecular O–H…O and N–H…O hydrogen bonds are involved in crystal structure stabilization. An intramolecular O–H…N hydrogen bond is observed between the phosphate OH group and the N atom. Further, the molecular Hirshfeld surface analysis was carried out to reveal the nature of intermolecular contacts and the fingerprint plot provides the information about the percentage contribution and reveals that the O…H (44.1%) interactions have the major contribution to form the crystal. The Mulliken population analysis and the HOMO-LUMO energy gaps show that the molecule has a good stability and from the calculation, we conclude that the molecule is really hard materials.
 
 KEY WORDS: Energy gaps, Hydrogen bonds, Hirshfeld surface, Mulliken population, Phosphate
 
 Bull. Chem. Soc. Ethiop. 2021, 35(3), 625-638.
 DOI: https://dx.doi.org/10.4314/bcse.v35i3.13

SSR-Based Molecular Identification and Population Structure Analysis for the Yunrui-Series Sugarcane (Saccharum spp. Hybrids) Genotypes

SSR-Based Molecular Identification and Population Structure Analysis for the Yunrui-Series Sugarcane (Saccharum spp. Hybrids) Genotypes

A novel acidic and SDS tolerant halophilic lipase from moderate halophile Nesterenkonia sp. strain F: molecular cloning, structure analysis and biochemical characterization

A novel acidic and SDS tolerant halophilic lipase from moderate halophile Nesterenkonia sp. strain F: molecular cloning, structure analysis and biochemical characterization

Growth, optical, electrical properties and DFT studies on piperidinium 4-nitrophenolate NLO single crystal in acetone

Piperidinium 4-nitrophenolate (P4NP) has been grown successfully with good optical quality and dimension of 35x5x3 mm3 in acetone solvent. The unit cell dimension and space group of grown P4NP crystal were examined by single crystal X-ray diffraction technique. We present experimental and theoretical studies on the molecular structure, nonlinear optical (NLO), electronic structural and UV spectral analysis for the grown crystal was determined using the density functional method (DFT/B3LYP) with a basis set of 6–311++G (d, p). The fluorescence spectral analysis was performed on P4NP crystal. The powder SHG efficiency of P4NP crystal was estimated and it is 1.86 times superior to the standard urea. Dielectric constant and complex impedance of P4NP were examined as a function of frequency at various temperatures. The computed HOMO and LUMO energies, DOS as well as the MESP, demonstrate that the charge transfer happens within the P4NP molecule. The computed findings were used to generate the UV spectra and nonlinear optical behavior of P4NP crystal which are in well accordance with the experimental results.